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26 May 2015

607. Ping...Topspin and ADF work on debian jessie

My blog post productivity has been getting increasingly poor over the past year and a half, with a precipitous dip occurring at the beginning of this year. The dip is due to teaching and research, and the slow but steady decline preceding it is due to parenthood (the older the little one gets, the less time -- and inclination! -- I have to do extra work. Toddlers can be so much fun.).

I've got a few posts that need a bit of polishing before I publish ('how to set up your own DNS server' and 'how to set up your own mail server' are two examples), but until then, I'll seed your google search results with the following information about something completely different:

* Bruker Topspin 3.2 (https://www.bruker.com/products/mr/nmr/nmr-software/software/topspin/overview.html) -- the NMR program, not the table tennis game -- installs fine on Debian Jessie 64 bit (the only version we tried). Note that:
** you'll need java
** you'll need the 32 bit package with libXtst.so.6, not the 64 bit package. It can be installed via apt-get install libxtst6:i386
** you'll need to enable the root account if you haven't already (the easiest way to do that is to do sudo passwd root, set a password and you're good to go)

* The trial version of the Amsterdam Density Functional package (ADF; http://www.scm.com/Downloads/2014) installs and runs fine* on one of my Debian Jessie 64 bit nodes. I did not install the intel mpi libraries, but then adf seems to be working according to a shared memory model.

Installation was quick and painless. I downloaded the package using the instructions in the email, copied the .tgz file to my node, ssh:d with X enabled (ssh -XC) to allow for interactive activation/registration, and to be able to use adfjobs (to draw molecules and set up jobs), and to be able to use adfview.

I untared the adf file:tar xvf adf2014.07.pc64_linux.intelmpi.tgz

I then moved the folder to /opt and took ownership of it:sudo mv adf2014.07 /opt/sudo chown $USER:$USER /opt/adf2014.07 -R

I edited /opt/adf2014.07/adfrc.sh to read:

ADFHOME=/opt/adf2014.07

And then sourced it and ran adfjobs:source adfrc.shbin/adfjobs

I was then asked to provide the username and password from my email, and from that point on it was just a matter of using the program (which has it's own quirks ).

*by default only six cores on a hex core i7-4930k are used. To force 12 cores (hyperthreading) you need to explicitly tell ADF to do so. The manual says not to, however. I haven't done any performance tests, BUT without specifying 12 cores the node is only running at half load.